Comparative and Joint Analysis of Two Metagenomic Datasets from a Biogas Fermenter Obtained by 454- Pyrosequencing
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Comparative and Joint Analysis of Two Metagenomic Datasets from a Biogas Fermenter Obtained by 454- Pyrosequencing Sebastian Jaenicke1, Christina Ander1, Thomas Bekel1, Regina Bisdorf1, Marcus Dro¨ ge2, Karl-Heinz Gartemann3, Sebastian Ju¨ nemann1,4, Olaf Kaiser2, Lutz Krause5, Felix Tille1, Martha Zakrzewski1, Alfred Pu¨ hler6, Andreas Schlu¨ ter6., Alexander Goesmann1*. 1 Computational Genomics, Center for Biotechnology (CeBiTec), Bielefeld University, Bielefeld, Germany, 2 Roche Diagnostics GmbH, Penzberg, Germany, 3 Department of Genetechnology/Microbiology, Bielefeld University, Bielefeld, Germany, 4 Department of Periodontology, University Hospital Mu¨nster, Mu¨nster, Germany, 5 Division of Genetics and Population Health, Queensland Institute of Medical Research, Herston, Australia, 6 Institute for Genome Research and Systems Biology, Center for Biotechnology (CeBiTec), Bielefeld University, Bielefeld, Germany Abstract Biogas production from renewable resources is attracting increased attention as an alternative energy source due to the limited availability of traditional fossil fuels. Many countries are promoting the use of alternative energy sources for sustainable energy production. In this study, a metagenome from a production-scale biogas fermenter was analysed employing Roche’s GS FLX Titanium technology and compared to a previous dataset obtained from the same community DNA sample that was sequenced on the GS FLX platform. Taxonomic profiling based on 16S rRNA-specific sequences and an Environmental Gene Tag (EGT) analysis employing CARMA demonstrated that both approaches benefit from the longer read lengths obtained on the Titanium platform. Results confirmed Clostridia as the most prevalent taxonomic class, whereas species of the order Methanomicrobiales are dominant among methanogenic Archaea. However, the analyses also identified additional taxa that were missed by the previous study, including members of the genera Streptococcus, Acetivibrio, Garciella, Tissierella, and Gelria, which might also play a role in the fermentation process leading to the formation of methane. Taking advantage of the CARMA feature to correlate taxonomic information of sequences with their assigned functions, it appeared that Firmicutes, followed by Bacteroidetes and Proteobacteria, dominate within the functional context of polysaccharide degradation whereas Methanomicrobiales represent the most abundant taxonomic group responsible for methane production. Clostridia is the most important class involved in the reductive CoA pathway (Wood-Ljungdahl pathway) that is characteristic for acetogenesis. Based on binning of 16S rRNA-specific sequences allocated to the dominant genus Methanoculleus, it could be shown that this genus is represented by several different species. Phylogenetic analysis of these sequences placed them in close proximity to the hydrogenotrophic methanogen Methanoculleus bourgensis. While rarefaction analyses still indicate incomplete coverage, examination of the GS FLX Titanium dataset resulted in the identification of additional genera and functional elements, providing a far more complete coverage of the community involved in anaerobic fermentative pathways leading to methane formation. Citation: Jaenicke S, Ander C, Bekel T, Bisdorf R, Dro¨ge M, et al. (2011) Comparative and Joint Analysis of Two Metagenomic Datasets from a Biogas Fermenter Obtained by 454-Pyrosequencing. PLoS ONE 6(1): e14519. doi:10.1371/journal.pone.0014519 Editor: Ramy K. Aziz, Cairo University, Egypt Received July 15, 2010; Accepted December 14, 2010; Published January 26, 2011 Copyright: ß 2011 Jaenicke et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. Funding: T. Bekel acknowledges financial support from the Bundesministerium fur Bildung und Forschung (BMBF), SysMAP project (grant 0313704). S. Jaenicke acknowledges financial support by the BMBF grant 0313805A ‘GenoMik-Plus’. S. Ju¨nemann was supported by the BMBF PathoGeno-Mik Plus project 0313801N. The METAEXPLORE grant of the European Commission (KBBE-222625) is gratefully acknowledged. These funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. M. Dro¨ge and O. Kaiser are employees of Roche Diagnostics GmbH; sequencing of the obtained DNA sample was funded by Roche Diagnostics GmbH. Competing Interests: Marcus Dro¨ge and Olaf Kaiser are employees of Roche Diagnostics GmbH, Germany. This does not affect the authors’ adherence to all the PLoS ONE policies on sharing data and materials. * E-mail: [email protected] . These authors contributed equally to this work. Introduction mentally compatible energy source [1,2]. Moreover, generation of energy from biogas relies on a balanced carbon dioxide cycle. In The fraction of renewable energy forms for energy supply is Germany biogas is mainly produced from energy crops such as constantly increasing since fossil fuels are running short and energy maize and liquid manure in medium-sized agricultural biogas production from fossil fuels brings about emissions of the plants [1]. The microbiology of biogas formation from organic greenhouse gas carbon dioxide which has implications on the matter is complex and involves interaction of different microor- climate. In this context the production of biogas by means of ganisms. In the first step of the digestion process, organic polymers fermentation of biomass becomes more and more important of the substrate such as cellulose, other carbohydrates, proteins and because biogas is regarded as a clean, renewable and environ- lipids are hydrolysed to low-molecular weight compounds [3–5]. PLoS ONE | www.plosone.org 1 January 2011 | Volume 6 | Issue 1 | e14519 Biogas Cellulolytic Clostridia and Bacilli are among other bacteria important FLX platform. This paper describes an integrated analysis of the for this step. Subsequently, fermentative bacteria convert low- GS FLX and the GS FLX Titanium datasets with the objective to molecular weight metabolites into volatile fatty acids, alcohols, and deepen the knowledge on the taxonomic structure and composi- other compounds which are then predominantly metabolised to tion of a microbial community involved in biogas production acetate, carbon dioxide and hydrogen by syntrophic bacteria [6– within an agricultural, production-scale biogas plant. Moreover, 11]. These latter compounds are in fact the substrates for methane the described analysis intends to elucidate the metabolic capacity synthesis which is accomplished by methanogenic Archaea [12,13]. of the community, functional roles of specific microorganisms and Hydrogenotrophic Archaea are able to reduce carbon dioxide to key organisms for the biogas production process. methane using hydrogen as an electron donor, whereas aceticlastic Archaea convert acetate to methane [14–18]. The biochemistry and Methods enzymology of methanogenesis is well known for model organisms, but the functioning of biogas-producing microbial communities on Total community DNA preparation and sequencing the whole is insufficiently explored. Community structures of Total community DNA of a biogas fermentation sample obtained biogas-producing microbial consortia were analysed for different from an agricultural biogas plant was prepared by a CTAB-based systems and settings including a thermophilic municipal biogas DNA-isolation method [36] as described recently. More detailed plant [19], a thermophilic anaerobic municipal solid-waste digester information on the origin of the fermentation sample is given in a [20], thermophilic upflow anaerobic filter reactors [21], a previous publication [33]. An aliquot of the DNA preparation that completely stirred tank reactor fed with fodder beet silage [22], a was recently used for whole genome shotgun sequencing on the two-phase biogas reactor system operated with plant biomass [23], Genome Sequencer (GS) FLX platform now served as template DNA an anaerobic sludge digester [24], mesophilic anaerobic chemostats for sequencing on the GS FLX Titanium platform. The sequencing [25,26], a packed-bed reactor degrading organic solid waste [27] library was constructed according to the protocol of the GS Titanium and many other habitats. Most of these studies were based on the General Library Prep Kit (Roche Applied Science). After titration of construction of 16S rRNA clone libraries and subsequent the library using the GS Titanium SV emPCR Kit, a full sequencing sequencing of individual 16S rRNA clones. The resulting nucleotide run was carried out on the GS FLX Titanium platform. sequences were then taxonomically and phylogenetically classified to deduce the structure of the underlying community. Also, mcrA Data normalization clone libraries were used to elucidate methanogenic archaeal To assess the overall comparability of the pyrosequencing communities of different habitats [28–32]. The mcrA gene encodes datasets obtained from the GS FLX and Titanium platforms, the the alpha subunit of methyl-coenzyme M reductase representing the average GC content of all reads was determined for each dataset. final enzyme in the methanogenesis pathway. Since mcrA is present For this, various Perl scripts were developed to determine the in all methanogenic Archaea analysed so far, it serves as a overall and individual GC content of the obtained reads.